alexgre

XI YANG

Data Scientist

Health Outcomes & Biomedical Informatics

College of Medicine

University of Florida

Personal Profile

I am currently working as a data scientist in the department of Health Outcomes and Biomedical Informatics @ University of Florida.

My research mainly focuses on developing novel deep learning-based algorithms for various clinical NLP tasks including protected health information (PHI) de-identification in clinical text, clinical information extraction from clinical narratives, and clinical knowledge representation learning. I am also working on projects of predictive modeling of disease risk and deep phenotyping using different machine learning methods.

I also enjoy writing, editing and reviewing research works in fields of biomedical informatics, machine learning, and chemistry.

As a programmer, Python is my major working programming language but I love Scala. I have contributed to many open source projects like Transformers, XLNet, Apache Spark.

Experience

Data Scientist, Department of Health Outcomes & Biomedical Informatics, University of Florida

2018.4-now

  • Project: De-identification of Clinical Notes in the UF IDR (UF CTSI); Role: core developer
  • Project:Utilizing Data from the Electronic Medical Record to Predict Alzheimer's and Dementia Risk (Flroida Ed and Ethel Moore Alzheimer’s Disease Research Program); Role: Data Scientist
  • Project: Natural Language Processing to Connect Social Determinants and Clinical Factors for Outcomes Research (PCORI); Role: Data Scientist
  • Project: : DR-KNOW: Improving Automated Diabetic Retinopathy Diagnosis Guided by Clinical Reports (UF CTSI); Role: Data Scientist
  • Project: Cancer therapy induced cardiotoxicity in the OneFlorida Consortium (UF CTSI); Role: Data Scientist

Developer, Department of Health Outcomes & Biomedical Informatics, University of Florida

2017.10-2018.4

  • Project: The Sample Size Shop - GLIMMPSE; Role: Operation and Maintenance Engineer

Research Assistant, Department of Chemistry, University of Florida

2011.8-2016.8

  • Project: iClick Synthesis of metallopolymers and Highly Emmisive Materials; Role: student RA
  • Project: Linking Metal Ions Via Inorganic Click (iClick); Role Student RA

Education

Master's in Computer Science

University of Florida

2015-2017


Ph.D. in Chemistry

University of Florida

2011-2016

Bachelor of Science in Material Chemistry

Nankai University

2007-2011


Publications

See my google scholar at Link


Review Activity

PC Member, Reviewer and Subreviewer

  • JAMIA – Oxford; 2019-now
  • Health Informatics Journal – SAGE; 2018-now
  • Journal of Chemical Information and Modeling – ACS; 2015-2016
  • AMIA Annual Symposium; 2019
  • The 4th International Workshop on Semantics-Powered Data Mining and Analytics; 2019
  • ACM International Conference on Bioinformatics, Computational Biology, and Health Informatics; 2018
  • The first International Workshop on Health natural Language Processing; 2018

Honors and Awards

2019 National NLP Clinical Challenges (n2c2) (Link)

2019

  • Ranked 3rd in Track-1 Clinical Semantic Textual Similarity
  • Ranked 5th in Track-2 Family History Extraction Task 1 NER
  • Ranked 3rd in Track-2 Family History Extraction Task 2 Relation Extraction

2018 National NLP Clinical Challenges (n2c2) – Track2 (Link)

2018

  • Ranked 3rd in Task 1 NER
  • Ranked 4th in Task 2 Relation extraction
  • Ranked 2nd in Task 3 End-to-end

NLP Challenges for Detecting Medication and Adverse Drug Events from Electronic Health Records (MADE1.0) (Link)

2018

  • Ranked 3rd in Task 1 NER

Florida Heterocyclic and synthetic IUPAC-sponsored Conference

2015

  • SYNFACTS Poster Prize

Key Skills

Tools

  • Amazon AWS
  • MySQL
  • MongoDB
  • Git
  • Travis-CI
  • Docker
  • Keras
  • Tensorflow
  • PyTorch
  • Spark
  • Linux

Programming Languages

  • Java
  • Python
  • SQL
  • R
  • Scala
  • shell

Professional

  • Proficient Writing and Presentation Skills
  • Strong Self-Learning and Self-Teaching Abilities